1) If Zone 1 irrigates area "A" and Zone 2 also irrigates area "A", then I would turn off Zone 2 and let just Zone 1 water Area "A".
2) Perhaps you might be describing Zone 1 and Zone 2 as in the same location but Zone 1 covers grass and Zone 2 covers trees and some grass.
In that case, you really have 2 areas. Treat them as separate zones.
3) Perhaps you might have Zone 1 that irrigates Area "A" and Zone 2 irrigates Area "A" and Area "B". This is what I have at my house.
In this case, there is no perfect way to solve the problem because the zone areas overlap.
What I did was dialed down Zone 1 and changed my heads in Zone 2 to not overlap all of Area "A".
I have an irregular shaped area on a slope with mostly clay soil and an irrigation company that wanted to save time and money on install.
The clay soil helps even out the irregular over/underwatering so my problem isn't too bad.
Hope this helps